enable-autoexec option not working in ubuntu blender
As explained here, the --python cli option will bypass the settings, allowing a script to alter the setting. You can set it in python with

bpy.context.user_preferences.system.use_scripts_auto_execute = True


Another way of setting preferences is the userpref.blend file. You can save one on your machine then copy it to your remote server. There are several places blender looks for the userpref.blend - LOCAL, USER, SYSTEM - in that order. If you manually install a pre-built copy then you can add your userpref.blend into the local folder which would be 2.76/config/userpref.blend next to blender itself. More likely you will want to add it to your home folder ~/.config/blender/2.76/config/userpref.blend If that fails you can also set environment variables with the paths to look for certain files.